@article{toms_barrangou_2017, title={On the global CRISPR array behavior in class I systems}, volume={12}, ISSN={["1745-6150"]}, DOI={10.1186/s13062-017-0193-2}, abstractNote={Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity.By utilizing a statistical framework and visual analytic techniques, we have been able to test several hypotheses about CRISPR loci in bacterial class I systems. Quantitatively, though CRISPR loci can expand to hundreds of spacers, the mean and median sizes are 40 and 25, respectively, reflecting rather modest acquisition and/or retention overall. Histograms uncovered that CRISPR array size displayed a parametric distribution, which was confirmed by a goodness-of fit test. Mapping the frequency of CRISPR loci on a standardized chromosome plot revealed that CRISPRs have a higher probability of occurring at clustered locations along the positive or negative strand. Lastly, when multiple arrays occur in a particular system, the size of a particular CRISPR array varies with its distance from the cas operon, reflecting acquisition and expansion biases.This study establishes that bacterial Class I CRISPR array size tends to follow a geometric distribution; these CRISPRs are not randomly distributed along the chromosome; and the CRISPR array closest to the cas genes is typically larger than loci in trans. Overall, we provide an analytical framework to understand the features and behavior of CRISPR-Cas systems through a quantitative lens.This article was reviewed by Eugene Koonin (NIH-NCBI) and Uri Gophna (Tel Aviv University).}, journal={BIOLOGY DIRECT}, author={Toms, Alice and Barrangou, Rodolphe}, year={2017}, month={Aug} }
 @article{reed_ferguson_peng_collier_bradburn_toms_fogel_baker_hamill_2015, title={Contact isolation is a risk factor for venous thromboembolism in trauma patients}, volume={79}, ISSN={["2163-0763"]}, DOI={10.1097/ta.0000000000000835}, abstractNote={BACKGROUND Contact isolation (CI) is a series of precautions used to prevent the transmission of medically significant infectious pathogens in the health care setting. Our institution’s implementation of CI includes limiting patient movement to the assigned room. Our objective was to define the association between CI and venous thromboembolism (VTE) at our Level I trauma center. METHODS Our institution’s prospective trauma database was retrospectively queried for all patients admitted to the trauma service between January 1, 2011, and December 31, 2012. Data including demographics, Injury Severity Score (ISS), preexisting medical conditions, injury type, and VTE development were collected. CI status data were obtained from our institution’s infection control database. &khgr;2 was used to examine the unadjusted relationship between CI status and VTE. As the groups were not equivalent, logistic regression was then used to examine the relationship between CI and VTE while adjusting for relevant covariates including sex, age, ISS, and comorbidities. RESULTS Of the 4,423 trauma patients admitted during the study period, 4,318 (97.6%) had complete records and were included in subsequent analyses. A total of 249 (5.8%) of the patients were on CI. VTE occurred in 44 patients (17.7%) on CI versus 141 patients (3.5%) who were not isolated (p < 0.0001; odds ratio, 6.0; 95% confidence interval, 4.1–8.6). With the use of lasso [least absolute shrinkage and selection operator] regression to adjust for patient risk factors, this relationship remained highly significant (p < 0.0001; odds ratio, 2.61; 95% confidence interval, 1.7–4.0). CONCLUSION CI, ISS, hospital length of stay, and cardiac comorbidity were associated with VTE. After adjustment for other risk factors, CI remained most strongly associated with VTE. Although any medical intervention may come with unintended consequences, the risks and benefits of CI in this population need to be reevaluated. Further study is planned to identify opportunities to mitigate this increased VTE risk. LEVEL OF EVIDENCE Prognostic/epidemiologic study, level III; therapeutic study, level IV.}, number={5}, journal={JOURNAL OF TRAUMA AND ACUTE CARE SURGERY}, author={Reed, Christopher R. and Ferguson, Robert A. and Peng, Yiming and Collier, Bryan R. and Bradburn, Eric H. and Toms, Alice R. and Fogel, Sandy L. and Baker, Christopher C. and Hamill, Mark E.}, year={2015}, month={Nov}, pages={833–837} }